The cleanliness of an industrial process affects its desirability and profitability. For several reasons, molecular manufacturing has the potential to be an extremely clean process. Precise and well-controlled chemistry should allow high yields of products. Some processes, especially mechanosynthetic methods, will produce valuable pure chemicals rather than sludge as byproducts. Flexible chemistry will allow reduced use of undesirable elements such as heavy metals, which also facilitates recycling. Precise fabrication of complex components will reduce the need for post-processing such as trimming and coating with their associated waste. The main pollutant from a mechanosynthetic manufacturing operation may be heat. Structural strength vs. energy input might be comparable to or better than aluminum refining. Active product functionality (computation and power handling) per manufacturing energy will be many orders of magnitude better than any technology available today.